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cTAKES 3.0 Links

Apache cTAKES web site
Documentation:

WARNING: Newer instructions

NOTE: The information here is largely for the ctakes 2.5 build process (eclipse based with some ant). ctakes 3.x under apache now uses a maven based build process. Please see the following web site for current build instructions: http://incubator.apache.org/ctakes/3.0.0/developer-guide-3.0

(should these instructions be copied into this wiki page?)
YES! The original contents were just a start to the page and it should be changed over into what it takes now for 3.0.
The user doc and the developer doc that started on the incubator site should both be moved here and the main site should point to this doc. The same groups should be covered, meaning developers using Eclipse or the command line.

These are instructions for installation of cTAKES for developers. With these instructions you can set up your development environment with cTAKES code, change or extend the code, compile the code, and deploy. If you simply want to be a user of the software, refer to the [cTAKES 3.0 User Guide].

Knowledge about what the cTAKES components do is not supplied by the install instructions. This is found in the cTAKES 3.0 Component Use Guide. There is no training or documentation (except for code comments) on the code itself. You must familiarize yourself with the components and then study the code on your own to be able to extend it.

In order to modify/compile the source code for a cTAKES component, developers must utilize either an IDE, such as Eclipse, or another editor of your choice. Follow the appropriate sections here depending upon your developer preferences.

Once you have compiled the code you can process documents with the cTAKES components. The documents upon which you can run cTAKES will take many forms. An example of doing this is covered in the Processing Documents section.

The expert instructions below are short and require a lot of prerequisite setup on your own. If you need more help then follow the step by step instructions.

Eclipse

Expert install instructions

Prerequisites: Java JDK 1.6+, Eclipse IDE 4.2+, subversive plugin (or svn equivalent with appropriate SVN team provider connectors), m2e plugin (or mvn equivalent)

  • Import Project > Maven > Checkout Maven Project from SCM and use: svn:https://svn.apache.org/repos/asf/incubator/ctakes/trunk
  • Select all projects.
  • Wait until Eclipse downloads and builds all of your projects (it may take up to 30 minutes depending on the machine).
    • The various build helpers should run jcasgen and builds the projects for you. There should not be any reason to run mvn install, etc.
  • (Optional) If you would like to launch the UIMA CVD or CPE GUI, run ctakes-clinical-pipeline/resources/launch/UIMA_<CVD | CPE>GUI--clinical_documents pipeline.launch

Step by step install instructions (for Eclipse)

Preparing Java

Step

Example

1. All forms of development require the Java SDK 1.6+. You can get it from java.com.

Make sure you get the proper version and install the SDK not just the Java Runtime environment.

To check if you have the SDK, look in the lib directory of the Java install and see if the file tools.jar is there. If there is a lib directory and there is a file by that name then you have the SDK.

To check if you have the proper version. Enter the command:
Windows and Linux: 

java -version


on any command line to see what version you have now. 

C:\>java -version
java version "1.6.0_20"
Java(TM) SE Runtime Environment (build 1.6.0_20-b02)
Java HotSpot(TM) Client VM (build 16.3-b01, mixed mode, sharing)

2. It is possible that some commands and programs can find the Java runtime that you want to be used but it is best to set the JAVA_HOME environment variable. Set the value of JAVA_HOME to the absolute path of the root of the Java Runtime environment that you want UIMA and cTAKES to use.
Windows:
Right-click on Computer > Properties > Advanced System Settings > Advanced tab > Environment Variables button > New button for System variables. Once the values are entered click OK until you are out of the dialog series.
Linux: 

export JAVA_HOME=<path>


Preparing Eclipse

If you are going to use Eclipse for development then follow these instructions.

Step

Example

1. Download and install Eclipse 4.2+.

(optional) It is recommended that you start a new workspace to keep your cTAKES projects separate from other work.

No example

2. Subversion Eclipse plug-in (based on Subversive site). We will use the one called "Subversive - SVN Team Provider"

Help -> Install New Software...
Select the current Eclipse release (in the case of Eclipse 4 it is Juno) for the "Work with" field: 

Juno - http://download.eclipse.org/releases/juno

Expand the Collaboration category.
Select "Subversive SVN Team Provider".
Click Next.
Click Next.
Agree to the license.
Click Finish.
Restart Eclipse.

3. Subversion team provider connectors 1.7+.

After restarting Eclipse a dialog will ask you to install an SVN Kit for the Team Provider.
Select SVN Kit 1.7 or greater.
Click Finish.
Click Next.
Click Next.
Agree to the license.
Click Finish.
Accept the security warning (if one appears).
Restart Eclipse.



4. Maven is already part of Eclipse, but more integration to Maven commands is needed.

Help -> Install New Software...
Select the current Eclipse release (in the case of Eclipse 4 it is Juno) for the "Work with" field: 

Juno - http://download.eclipse.org/releases/juno

Expand the Collaboration category.
Select "m2e - Maven Integration for Eclipse".
Click Next.
Click Finish.
Restart Eclipse.

5. Maven SCM connector.

File -> Import ... -> Maven -> Check out Maven Projects from SCM.
Click Next.
Click the "m2e Marketplace" link.
You are now in the m2e Marketplace not the Eclipse Marketplace.
Scroll to and select m2e-subversive.
Click Finish.
Leave the defaults to install the "Maven SCM Handler for Subversive" and click Next.
Click Next.
Accept the license.
Click Finish.
Accept the security warning (if one appears).
Restart Eclipse.



Compile the latest stable release in Eclipse

Step

Example

1. Import the cTAKES projects using Maven.

File -> Import ... -> Maven -> Check out Maven Projects from SCM.
Click Next.


2. For SCM URL use "svn" in the drop-down 

https://svn.apache.org/repos/asf/incubator/ctakes/trunk

in the text field.
Click Finish.
Eclipse will download and builds all of the cTAKES projects including running jcasgen as needed. It may take up to 30 minutes depending on your machine and Internet speed.

Process documents using cTAKES

You can now launch or debug the cTAKES components that you have built. You could run commands from a command prompt, as found in the [user install instructions], but you can launch them from within Eclipse now instead. Launching the CAS Visual Debugger (CVD) and the Collection processing engine (CPE) from Eclipse is as simple as following this step.

Step

Example

1. Launch the UIMA CAS Visual Debugger (CVD) or the Collection Processing Engine (CPE). 

ctakes-clinical-pipeline/resources/launch/UIMA_<CVD | CPE>GUI--clinical_documents pipeline.launch

where you must select between CVD and CPE in the command.


(Optional) UIMA tools plug-in (for Eclipse)

Developers may be interested in the Eclipse plug-ins provided by the UIMA community. For example, they include a UIMA component descriptor editor.

Step

Example

1. Find UIMA Eclipse plug-ins.

Help> Install New Software...> Add... button
Set a repository name and this site location 

http://www.apache.org/dist/uima/eclipse-update-site


Click OK.

Unable to render embedded object: File (cTAKES_Win_UIMA_Repository.jpg) not found.

2. Install UIMA Eclipse plug-ins.

Select the UIMA Eclipse tooling and runtime support.
Click *Next >*and finish the install.

Additional help can be found on the Apache site UIMA for Eclipse on apache.org.

Unable to render embedded object: File (cTAKES_Win_UIMA_Repository_Install.jpg) not found.

(optional) Verify the installation of the UIMA Plug-ins. Go to Help> About Eclipse> Installation Details> Plug-ins. You will see a dialog such as that on the right (next cell) with plug-in names starting with "UIMA Eclipse:".

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Command line

Expert install instructions

Prerequisites: Java JDK 1.6+, SVN, Maven 3.0+

  • svn co https://svn.apache.org/repos/asf/incubator/ctakes/trunk ctakes
  • mvn clean compile package
    • Running the mvn package command will generate a binary distribution in /ctakes-distribution/target/ctakes-
      Unknown macro: {release}
      -bin.tar.gz/zip
  • (Optional) If you would like to launch the UIMA CVD or CPE GUI, run $ MAVEN_OPTS="-Xmx1g" mvn -PrunCVD compile

For further information see the Apache Source Code Repository page.

Step by step install instructions (for command line)

Preparing Command Line Tools

If you are going to use command line only to compile then you will need these tools.

Step

Example

1. Navigate to the Ant download site on apache.org and install Ant 1.7.1+

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2. Download Ant 1.7.1+. Unzip the file you downloaded to a local directory. We will call this <ANT_HOME> Follow the instructions for installing Ant on apache.org. This will include changing the PATH and ANT_HOME environment variables.

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The UIMA command to generate the type system through the command line (JCasGen) is not shipped with cTAKES at this time. The common type system has already been generated for you. If you need, for some reason, to generate this then you will need to use the method described for Eclipse or install the entire UIMA SDK.

Step

Example

1. Follow the first steps of the "Compile the latest stable release in Eclipse" (which do not require Eclipse) until you get to the part about creating a new project in Eclipse.

No example

2. Obtain the relevant build.xml file from SVN, placing it into <cTAKES_HOME>

It can be found at https://ohnlp.svn.sourceforge.net/svnroot/ohnlp/trunk/icTAKES/build.xml
Be aware there are multiple build.xml files in SVN. be sure to use the one listed above

No example

3. To compile cTAKES, change to the <cTAKES_HOME> directory and simply run: 

ant

No example

Process documents using cTAKES

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